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Your donation can be recorded in our online journal. Over the last 20 years Edinburgh has lost over 2, street trees. They frame our most famous landmarks and tower over our parks, but like all living things they eventually die. It takes years for a tree that is planted today to be as large as a year old specimen.. Find out more. Tree Time Tree Time is a great way to help replace the trees that have been lost in your local streets. Your local community will be contributing t Read More. We received some lovely feedback from residents who fundraised to get trees planted in their local neighbourhood. We were delighted to receive some feedback from local residents about the new trees that have been planted in Boswall.
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction. GitHub is home to over 50 million developers working together to host and review code, manage projects, and build software together. Work fast with our official CLI. Learn more. If nothing happens, download GitHub Desktop and try again.
Mutations that accumulate in the genome of cells or viruses can be used to infer their evolutionary history. In the case of rapidly evolving organisms, genomes can reveal their detailed spatiotemporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly evolving viral pathogens. As the number of genome sequences available for different pathogens has increased dramatically over the last years, phylodynamic analysis with traditional methods becomes challenging as these methods scale poorly with growing datasets. Here, we present TreeTime, a Python-based framework for phylodynamic analysis using an approximate Maximum Likelihood approach. TreeTime can estimate ancestral states, infer evolution models, reroot trees to maximize temporal signals, estimate molecular clock phylogenies and population size histories. The runtime of TreeTime scales linearly with dataset size. Phylogenetics uses differences between homologous sequences to infer the history of the sample and learn about the evolutionary processes that gave rise to the observed diversity. In absence of recombination, this history is a tree along which sequences descend from ancestors with modification.